NM_004287.5(GOSR2):c.1A>G (p.Met1Val) AND Progressive myoclonic epilepsy

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 25, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV001371323.10

Allele description [Variation Report for NM_004287.5(GOSR2):c.1A>G (p.Met1Val)]

NM_004287.5(GOSR2):c.1A>G (p.Met1Val)

Genes:

GOSR2:golgi SNAP receptor complex member 2 [Gene - OMIM - HGNC]
LRRC37A2:leucine rich repeat containing 37 member A2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

17q21.32

Genomic location:

Preferred name:

NM_004287.5(GOSR2):c.1A>G (p.Met1Val)

HGVS:

NC_000017.11:g.46923193A>G
NG_031806.2:g.5074A>G
NM_001012511.3:c.1A>G
NM_001321133.2:c.1A>G
NM_001321134.2:c.-102A>G
NM_001330252.2:c.1A>G
NM_001353114.2:c.1A>G
NM_001353115.2:c.1A>G
NM_001353116.2:c.1A>G
NM_001363851.2:c.-465A>G
NM_004287.5:c.1A>GMANE SELECT
NM_054022.4:c.1A>G
NP_001012529.1:p.Met1Val
NP_001308062.1:p.Met1Val
NP_001317181.1:p.Met1Val
NP_001340043.1:p.Met1Val
NP_001340044.1:p.Met1Val
NP_001340045.1:p.Met1Val
NP_004278.2:p.Met1Val
NP_473363.1:p.Met1Val
NC_000017.10:g.45000559A>G
NM_004287.3:c.1A>G
NR_148349.2:n.34A>G
NR_148350.2:n.34A>G
NR_148351.2:n.34A>G

Protein change:

M1V

Links:

dbSNP: rs879328855

NCBI 1000 Genomes Browser:

rs879328855

Molecular consequence:

NM_001321134.2:c.-102A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001363851.2:c.-465A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001012511.3:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001321133.2:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001330252.2:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001353114.2:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001353115.2:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001353116.2:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_004287.5:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_054022.4:c.1A>G - initiator_codon_variant - [Sequence Ontology: SO:0001582]
NM_001012511.3:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001321133.2:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330252.2:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353114.2:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353115.2:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001353116.2:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_004287.5:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_054022.4:c.1A>G - missense variant - [Sequence Ontology: SO:0001583]
NR_148349.2:n.34A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148350.2:n.34A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148351.2:n.34A>G - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Progressive myoclonic epilepsy
Synonyms:: Myoclonic Epilepsies, Progressive; Familial progressive myoclonic epilepsy; Progressive myoclonus epilepsy; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0020074; MedGen: C0751778; Orphanet: 308; OMIM: PS254800

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001567881	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Apr 25, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001567881

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Apr 25, 2022)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001567881.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

This sequence change affects the initiator methionine of the GOSR2 mRNA. The next in-frame methionine is located at codon 19. This variant is present in population databases (no rsID available, gnomAD 0.008%). This variant has not been reported in the literature in individuals affected with GOSR2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1061696). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 24, 2024

ClinVar

Relating variation to medicine